Phase III Update
So I have started building Phase III, but due to my inexperience with ancient history, took a long time. Right now only Athens has been reworked. It is playable, but AI cannot upgrade building yet so it is recommended to not assign AI to Athenians for now. This should be compatible with current version of City Building Mod, but it is recommended to play it separately as I haven't tested the integration fully.
Notable changes:
Phasing is now automatic, but Agora still has to be upgraded first, from Village center to Town center to City center.
Market and Fortress are now unbuildable, but upgradable from buildable village center.
Agora can now trade, so bartering can be done in village phase.
Athens can now build Siege Workshop and Stable.
New units and technologies based on social class.
and more.
Enjoy and let me know if there's some bug or some gameplay changes that don't make sense.
Citizen-Mod.zip

Great!
My suggestion is that I think 0 A.D. wiki can be a great baseline for your project, at least the outline can be used. If you're going this way, then it should be easier since you don't have to work from scratch. You just have to add what you think should be added and remove irrelevant parts, for example historical background, i.e. why this faction is in-game, why are they represented by these units, etc.
If these seem overwhelming to you and seemingly required extensive research, worry not, as it was already researched by 0 A.D. team right here in this very forum. References on historical background and concept art, discussion on gameplay designs and balance, it's all here. It is just a matter of finding the correct threads and extracting the knowledge for public consumption.
I believe the guidebook you're trying to create will be very useful, as it will not only help players to understand the game, but also rope people who are interested in the history to play this game. Even game devs could potentially integrate your guide into the game in many ways.
The problem is that this game right now is still unfinished, so any detailed information about gameplay could potentially be obsolete at any time. So my suggestion is to focus less on the gameplay and more to the historical background and concept arts.

Hi @Syn! I think this is a great idea. Is this book intended to be an e-book or physical book as well? I imagine game guide like the ones included in many old RTS games, a mix of brief historical introductions and gameplay guide.
Have you seen 0 A.D. Wiki? It seems to have similar goals with you, although this is very light on historical facts and more like brief information of game components.

How about different alert based on territory? So if your building/unit is attacked in your territory, then the alert would be "Your territory is attacked by <enemy>", to differentiate it from existing alert, which will only be used if your units are attacked outside of your territory (e.g. when attacking or scouting).

So it is similar to the system in Age of Mythology/Age of Empires III, I assume?
I know it is not 100% what you want, but have you take a look at Upgrade component? The example of its implementation in the game is Sentry Tower, upgradable to bigger Defense Tower. Its function is to change an entity to another with certain cost and technology. You can even upgrade a building into a unit and vice versa, as seen in Terra Magna/Delenda Est Nomad factions where tents can be upgraded to wagons and back to tents. You're gonna have to create three separate civic centers for that to work though, each with different heroes and technologies. And the Upgrade button is placed in upper rows with other trainable units and not lower with other technologies. Also there's no fancy selection dialog box.
These are good but the selection choice is triggered in the beginning of the game. There need to be modification to trigger the selection on phasing.
OTT but how did you make the mockup? Is that SketchUp?

If I understood this correctly, the percentage is the final result, therefore it is the one that should be displayed in the tooltip. The base level and other things could be elaborated more in right click detail. Tooltip should not make player think too much.

Hi,
I already tried it. It is honestly a great improvement of the original. The instruction is much more compact compared to a wall of text of the original. I also love the way you can minimize the tutorial box when you press OK. I have some suggestion I'd like to share.
I'm still torn between the interface of this tutorial and the transparent interface of the original. I feel the black background makes it easier to read but it is covering a quarter of my screen. The transparent original is hard to read but doesn't feel as claustrophobic.
When the instruction is to batch train Slingers, any other unit seems to be disabled, even training single slinger. I think there should be a notification to tell player if they click the wrong button, like "You just selected a button to Train Woman, please press [Shift] and select Slingers" or "You haven't hold [Shift] button before selecting Slingers, please press [Shift] and select Slingers".
Is it possible to have some ways to point a part of the screen to aid the player? Like flashing buttons or arrows to make it clearer.
How about adding some backstory of the tutorial for context? Making it like a mini campaign with historical background, just like its predecessor like Age of Empires series and Empire Earth. I just read up about Spartacus and it seems to be an interesting part of history that can be adapted. Age of Empires II introduction and tutorial can be a good example.

From @Nescio's description and my brief research, Stoa is basically just part of Agora. Even the model of Hellenes' Agora consists of a Stoa and a fountain in its front yard. It makes more sense as an embassy indeed.
However if in the future 0 A.D decided to have different actor for civic center for different phases, the actors can come in handy. It is a nice progression from Stoa > Royal Stoa > Agora for Village > Town > City.

I'd like to share my opinion on mercenaries.
I agree with @Lion.Kanzen that Mercenary Camps shouldn't be buildable. It should be neutral and capturable.
However for Allied/Auxiliary units it should be a separate building. I think every faction should have its own Embassy building that trains foreign non-mercenary units. Similar to Carthage's Embassy but only one instead of three kinds. But it should still work like mercenary camps, i.e. when captured it should be able to train native troops instead of faction troops like Barracks.

I have come to think of current UI as an accepted reality, but seeing this, I know it could be improved a lot more.
Simplifying it further with icons also works well with this.
At least on the tooltip. We can have more liberty to explain what each icon means in the Detail (right click) window right? Just my two cents.
Hack, Pierce, and Crush should be replaced with icons as well, I just don't know how the icons should look like.